Burger Albert, Davidson Duncan, Baldock Richard
MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, Scotland, UK.
Bioinformatics. 2004 Jan 22;20(2):259-67. doi: 10.1093/bioinformatics/btg400.
The Edinburgh Mouse Atlas and Gene Expression Database project has developed a digital atlas of mouse development to provide a spatio-temporal framework for spatially mapped data such as in situ gene expression and cell lineage. As part of this database, a mouse embryo anatomy ontology has been created. A formalization of this anatomy is required to document its precise semantics and how it is used in the context of the Mouse Atlas.
The paper describes the existing anatomy ontology and formalizes aspects of it using a predicate logic based approach. It therefore provides a guide for users of the current version of the ontology, as well as the basis for a description of the anatomy using an ontology language, such as OWL, thus enabling future work on reasoning about the Mouse Atlas in the context of an intelligent gene expression bioinformatics workflow system. The logic has been implemented in a Prolog prototype.
The Mouse Atlas is available on-line at http://genex.hgu.mrc.ac.uk
爱丁堡小鼠图谱与基因表达数据库项目已开发出一个小鼠发育数字图谱，为诸如原位基因表达和细胞谱系等空间映射数据提供时空框架。作为该数据库的一部分，已创建了一个小鼠胚胎解剖本体。需要对这种解剖结构进行形式化，以记录其精确语义以及它在小鼠图谱背景下的使用方式。
本文描述了现有的解剖本体，并使用基于谓词逻辑的方法对其进行形式化。因此，它为当前版本本体的用户提供了指南，也为使用诸如OWL等本体语言描述解剖结构奠定了基础，从而能够在智能基因表达生物信息学工作流程系统的背景下开展关于小鼠图谱推理的未来工作。该逻辑已在Prolog原型中实现。
